Supplementary Material for: New insights into chromosomal regions 15p11.2 to 15q11.2 by studying submicroscopic variations using molecular cytogenetics

Introduction: The chromosome region 15p11.2 to 15q11.2 contains heterochromatic and euchromatic DNA segments. Heteromorphisms in 15p11.2 to 15q11.1 have been reported, as has been a euchromatic variant region (EV) in 15q11.2.
Methods: Fluorescence in situ hybridization (FISH) was used to examine the genomic regions 15p11.2 to 15q11.2 in parallel and at the single-cell level. A total of 44 cases with normal chromosomes 15 were examined, including 38 cases with a small supernumerary marker chromosome 15 (sSMC(15)). A combined five-color FISH probe set A and B was developed, which includes probe mixtures for the positions 8.7 to 20.7 Mb and 22.262115 to 23.863963 Mb (GRCh37/hg19).
Results: Therefore, the frequencies of the 15p11.2- to 15q11.1-heteromorphisms for D15Z1, D15Z3 and D15Z4 were determined at 16%, 7.4% and 13.5%, respectively. Copy number gains or losses in the EV region 15q11.2 were most frequently observed at positions 22.262115-22.826598 (GRCh37/hg19); overall, copy number variants in 15q11.2 were observed in 41% of the chromosomes 15 examined. Furthermore, it became clear that more attention needs to be paid to the exact characterization of breakpoints in sSMC(15) cases. It was shown that the breakpoint clusters involved in sSMC formation differ from those responsible for microdeletions associated with Prader-Willi/Angelman syndrome. Interestingly, at least 25% of the sSMC(15) cases studied here were formed by an interchromosomal U-type exchange. This group also included two previously unrecognized asymmetric sSMCs.
Conclusion: In summary, the detailed investigation of the chromosomal regions 15p11.2 to 15q11.2 using molecular cytogenetics has provided new insights into the formation of sSMC(15) and submicroscopic variations in this region.